Caister Academic Press

Figure from the book: Hepatitis C Viruses: Genomes and Molecular Biology

Hepatitis C virus

Chapter 11. Fig. 1.
Structure of the HCV genome and Con1-derived bicistronic replicon, location of adaptive mutations in the HCV polyprotein of subgenomic replicons, and the positions of these mutated residues in the crystal structures of the NS3 protease, the NS3 helicase, and the NS5B RdRp. (A) (Top) Schematic of the complete HCV genome. The 5' and 3' NTRs flank the ORF (open box) with the structural proteins located in the N-terminal portion of the polyprotein and the remainder encoding the non-structural proteins. (Bottom) Structure of the selectable Con1 bicistronic replicon composed of the 5' NTR, the first 12 amino acids of the capsid-coding region (open box) fused to the Neo gene (Neo; black box), the EMCV IRES (EMCV; solid line), the NS3-5B coding region (open box), and the 3' NTR structure. (B) Schematic representation of the NS3 to NS5B coding region, sufficient for autonomous replication of subgenomic replicons in Huh-7 cells. The protease (P) and helicase (H) domains of NS3 are indicated along with the locations of the ISDR (shaded box) and the adaptive 47 amino acid deletion. The highly adaptive mutations in NS4B, NS5A, and NS5B and the amino acid substitutions in NS3 that act synergistically with these mutations to enhance subgenomic replication are shown to the right of the HCV NS3-5B polyprotein. The highly adaptive S2204I substitution in NS5A is highlighted in bold and those residues in NS3 (E1202G and T1280I) and in NS4B (K1846T) or NS5A (S2197P) that synergistically enhance replication are shown in italics. (C) Space-filling view of the NS3/4A serine protease (Protein Database 1A1R; Kim et al., 1996). The adaptive mutations depicted in panel B, the position of the active-site residues and the location the NS4A cofactor peptide are indicated. (D) The 3D structure of the NS3 helicase domain complexed with a single-stranded DNA oligonucleotide (Protein Database 1A1V; Kim et al., 1998). The oligonucleotide, the conserved DECH motif implicated in coupling NTP hydrolysis to nucleic acid unwinding, and the adaptive mutations are highlighted. Residue G1304 is partially buried in the molecule and therefore is not visible in the space-filling model shown. (E) Space-filling model of the NS5B RdRp ectodomain (Protein Database 1C2P; Lesburg et al., 1999). The putative RNA binding groove is labeled and the adaptive mutation is highlighted.